1N5X

Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An Extremely Potent Inhibitor of Xanthine Oxidoreductase: Crystal Structure of the Enzyme-Inhibitor Complex and Mechanism of Inhibition

Okamoto, K.Eger, B.T.Nishino, T.Kondo, S.Pai, E.F.Nishino, T.

(2003) J Biol Chem 278: 1848-1855

  • DOI: 10.1074/jbc.M208307200
  • Primary Citation of Related Structures:  
    1N5X

  • PubMed Abstract: 
  • TEI-6720 (2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid) is an extremely potent inhibitor of xanthine oxidoreductase. Steady state kinetics measurements exhibit mixed type inhibition with K(i) and K(i)' values of 1.2 +/- 0.05 x 10( ...

    TEI-6720 (2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid) is an extremely potent inhibitor of xanthine oxidoreductase. Steady state kinetics measurements exhibit mixed type inhibition with K(i) and K(i)' values of 1.2 +/- 0.05 x 10(-10) m and 9 +/- 0.05 x 10(-10) m, respectively. Fluorescence-monitored titration experiments showed that TEI-6720 bound very tightly to both the active and the inactive desulfo-form of the enzyme. The dissociation constant determined for the desulfo-form was 2 +/- 0.03 x 10(-9) m; for the active form, the corresponding number was too low to allow accurate measurements. The crystal structure of the active sulfo-form of milk xanthine dehydrogenase complexed with TEI-6720 and determined at 2.8-A resolution revealed the inhibitor molecule bound in a long, narrow channel leading to the molybdenum-pterin active site of the enzyme. It filled up most of the channel and the immediate environment of the cofactor, very effectively inhibiting the activity of the enzyme through the prevention of substrate binding. Although the inhibitor did not directly coordinate to the molybdenum ion, numerous hydrogen bonds as well as hydrophobic interactions with the protein matrix were observed, most of which are also used in substrate recognition.


    Related Citations: 
    • Hypouricemic effect of the novel xanthine oxidase inhibitor, TEI-6720, in rodents
      Osada, Y., Tsuchimoto, M., Fukushima, H., Takahashi, K., Kondo, S., Hasegawa, M., Komoriya, K.
      (1993) Eur J Pharmacol 241: 183

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-0022, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xanthine DehydrogenaseAB1331Bos taurusMutation(s): 0 
Gene Names: XDH
EC: 1.1.1.204 (PDB Primary Data), 1.17.1.4 (UniProt), 1.17.3.2 (UniProt)
Find proteins for P80457 (Bos taurus)
Explore P80457 
Go to UniProtKB:  P80457
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MTE
Query on MTE

Download CCD File 
A, B
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
 Ligand Interaction
TEI
Query on TEI

Download CCD File 
A, B
2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-METHYL-5-THIAZOLE-CARBOXYLIC ACID
C16 H16 N2 O3 S
BQSJTQLCZDPROO-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

Download CCD File 
A, B
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TEIIC50:  25   nM  BindingDB
TEIKi:  0.10000000149011612   nM  BindingDB
TEIKi:  120   nM  BindingDB
TEIIC50:  30   nM  BindingDB
TEIIC50:  20   nM  BindingDB
TEIIC50:  19   nM  BindingDB
TEIIC50:  5.199999809265137   nM  BindingDB
TEIIC50:  13   nM  BindingDB
TEIIC50:  1.2999999523162842   nM  BindingDB
TEIIC50:  4   nM  BindingDB
TEIIC50:  3   nM  BindingDB
TEIKi:  900   nM  BindingDB
TEIIC50:  10   nM  BindingDB
TEIIC50:  30   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.269α = 90
b = 124.659β = 90.99
c = 147.325γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-05-08
    Changes: Other